BIO 112 Lab 1

A major theme of this course, both in the classroom and in the lab, is diversity. Throughout this course we will encounter the spectacular biological diversity (“biodiversity”) of Earth and consider the differences and similarities among the major groups of organisms. Then in labs 6-10 we study the diversity of organ systems and learn how organisms function. Since there are between 5 and 30 million species on Earth, we are immediately confronted with two important issues: 1) how do we classify and name all of these species?, and 2) how did this remarkable biodiversity arise? In today’s laboratory session you will practice using the tools of the related endeavors of taxonomy and systematics, two fields that help biologists classify species and determine their evolutionary relationships.

The term taxonomy is derived from the Greek taxis (meaning 'arrangement') and nomos (meaning ‘law’). Taxonomy can be defined as the theory and practice of classifying organisms. Classification is vital in order to make the bewildering array of organic diversity available to workers in other disciplines where proper identification of organisms is vital, e. g. ecology, fishery biology, medical parasitology, molecular biology. Systematics, from the latinized Greek systema (meaning 'an ordered arrangement') can be defined as the theory and practice of the scientific study of the kinds and diversity of organisms and of all of the relationships among them. These relationships include, but are not limited to, evolutionary or phylogenetic relationships. Defined in this way systematics is a large and synthetic discipline that properly includes taxonomy as well as ecology, genetics, developmental biology, and nearly every other subdiscipline of biology.

One of the major goals of biology is to establish working phylogenies of all living things. The term phylogeny is derived from the Greek phylon (meaning 'race' or 'kind') and geneia (meaning 'origin') and refers to the evolutionary descent of a single organism or group of organisms. The sciences of taxonomy and systematics are central to the study of the phylogenetic (evolutionary) relationships that exist among organisms. While sometimes confused or considered synonyms of each another, these two disciplines can be seen as separable, yet related.

The fundamental unit of taxonomy is the species. Each species has a unique Latin binomial, consisting of a genus name and the specific epithet that follows, e.g., Homo sapiens, the human species. Note that by convention the genus (plural: genera) is always capitalized and that the entire Latin name is either italicized or underlined. The Latin names of species may be derived from classical Greek or Latin names (e.g., Homo = man), or they may be descriptive terms (e.g., sapiens = wise). Sometimes, the binomial is followed by an abbreviation for the “authority,” or taxonomist who first applied that name to that particular species. For example, in Liriodendron tulipifera L., “L.” stands for Linnaeus, the father of modern taxonomy and the man who named the tulip tree, which we will encounter in today’s lab.

In making the diversity of organisms available to workers in other fields, taxonomists will often produce a dichotomous key to a particular group of organisms. Many times these keys are designed to work for a particular group from a particular area, e.g. a key to the trees and shrubs of eastern North America or a key to the beetles of the family Carabidae from Peru. The best keys are those that can be used by specialists and non-specialists alike, although the latter group might need to become familiar with a set of specialized terms that relate to the morphology, ecology, etc. of the group under consideration.

Dichotomous keys are groups of pairs (couplets) of choices that relate to specific characters displayed by the organisms that the key is designed to treat. A character is any feature of an organism that can be measured in some way. These are often morphological/anatomical features (e. g. number of appendages, type of coelom, presence of a vascular tissue) but can also include behavioral features such as songs in the case of birds, color, or ecological features such as the time of day an organism is active (nocturnal, crepuscular, etc.). The most helpful characters in terms of identifying organisms are those that have more than one state represented among the group of organisms under study. A character state is defined as an alternate form of a particular character. For example, if the character is the arrangement of leaves on a plant stem, then opposite, alternate, and whorled are all character states for this one character. Leaf arrangement then is a multistate character, because it can appear in more than one state. Another example would be the shape of the edge of a leaf. This single character could have multiple states: smooth, wavy, saw-tooth, etc. Dichotomous keys proceed by giving the user a choice between two different characters, character states, or groupings of characters and character states. Each choice of the two (hence the use of the term dichotomy) leads the user through the key until finally the last couplet leads to the name of the organism at hand.

Most identification keys are said to be “artificial,” meaning that they do not necessarily reflect the true evolutionary relationships, or phylogenies, of organisms. The phylogeny of any group of organisms is most commonly thought of as an evolutionary tree wherein the branching pattern of the tree indicates the evolutionary relatedness among the member taxa. A key, although it also has a branching structure, is merely a convenient device for distinguishing one species from another; therefore, the branching patterns of a key and a phylogeny will often not coincide with one another. An illustrative example is taken from the Key to Wesleyan College Trees that follows. Southern magnolia and tulip tree are closely related, evolutionarily, and are therefore placed in the same family, Magnoliaceae, the magnolias. However, in the artificial key, these species do not key out close to each other because the southern magnolia is evergreen and the tulip tree is deciduous.

Lab 1 Worksheet

PART I. USE OF DICHOTOMOUS KEYS.

As described below, practice using the dichotomous key in the blue area below to identify common local woody plants.

Materials:

Dichotomous key to selected woody plants of Wesleyan College.
Herbarium specimens of the plant species.

Dichotomous key to the insects.
Mounted insect specimens from Wesleyan's invertebrate collection.

A. Using a "nested key" to identify plant species

Procedure:

1. Starting at any specimen, attempt to identify it by following each option presented in the Plant Dichotomous Key below until all choices end.

2. Be able to recognize all specimens, as well as their distinguishing characteristics.

Study suggestions:

1. Make detailed sketches and notes on specimens. This will help you to look at the specimens more closely, as well as to help you study later.

2. Plan to come view the specimens once or twice more before the lab test. Test yourself by attempting to identify the specimens using the key.

KEY TO SELECTED WOODY PLANTS OF WESLEYAN COLLEGE

Note: this key includes only 10 species, about 10 percent of the woody plant diversity in the Wesleyan College Arboretum. The key will therefore not work, or may give an erroneous result, if used to identify a species not included in the key. More complete keys are available from the Biology Department and in books about Georgia trees.

1. Trees; bearing woody cones with seeds naked (not enclosed in ovary); leaves evergreen or deciduous; leaves needle-like or scale-like:

2. Deciduous; leaves short, scale-like; cones 2-3 cm, disintegrating when mature; woody “knees” at or near base of tree; wetlands Baldcypress (Taxodium distichum)

2. Evergreen; leaves long (15 cm), needle-like, in bundles of 3; cones 10-15 cm, persistent; “knees” absent; uplands Loblolly Pine (Pinus taeda)

1. Trees or shrubs; bearing true fruits (fleshy or dry) with seeds enclosed in ovary; leaves evergreen or deciduous; broad-leaved

2. Leaves evergreen

3. Leaves opposite on twigs; shrub, parasitic on trees; berries white
American Mistletoe (Phoradendron serotinum)

3. Leaves alternate on twigs; trees; fruit or seeds red

4. Leaves 15-20 cm; margins smooth, untoothed; leaves brown-hairy below; fruit a cone-like aggregate, ca. 10 cm; seeds with red fleshy coat Southern Magnolia (Magnolia grandiflora)

4. Leaves 5-8 cm; margins with sharp prickles; leaves hairless below; fruit red berries American Holly (Ilex opaca)

2. Leaves deciduous (or tardily deciduous)

3. Leaves or buds opposite on twigs

4. Twigs and buds reddish; buds with many overlapping scales; buds similar in size; fruit dry, winged Red Maple (Acer rubrum)

4. Twigs and buds green; buds with two scales; larger, globular flower buds may be present; fruit fleshy, red Flowering Dogwood (Cornus florida)

3. Leaves or buds alternate on twigs

4. Buds clustered at tips of twigs; some leaves may persist in winter; fruit an acorn Water Oak (Quercus nigra)

4. Buds not clustered at tips of twigs; fruit a spiky ball or a cone-like aggregate; seeds winged

5. Buds with many overlapping scales; twigs lacking scars encircling twigs at leaf scars; twigs may have corky “wings”; fruit a spiky ball with 1 cm winged seeds
Sweetgum (Liquidambar styraciflua)

5. Buds with two scales; twigs with scars encircling twigs at leaf scars; twigs lacking corky “wings”; fruit a cone-like aggregate of 3 cm winged seeds Tulip Tree (Liriodendron tulipifera)

B. Using a "go to" key to classify insect orders

Procedure:

1. Use the Dichotomous.Key to the Insects to classify the sample insect at your station

2. As time permits, collaborate with the other student groups to classify their samples.

Study suggestions:

1. This key will use a lot of terms which will be unfamiliar to you. Ask the instructor of course assistant for help understanding those terms, or look up definitions online as you go.

2. You will not be responsible for remembering the classification of these insect samples. However, you will be responsible for understanding how to use this type of "go to" key.

PART II. RECONSTRUCTING PHYLOGENY

Determining the branching evolutionary history of any group of organisms is a daunting task that requires evidence of many different types. Systematists rely on the following sources of evidence: molecular data (amino acid sequences of proteins, DNA sequences), fossils, biogeography, embryology, and morphology. In this exercise you will attempt to reconstruct the phylogeny of a group of hypothetical trees based strictly on their morphology. A similar exercise could be designed using molecular data but the concepts of homology and parsimony are easiest to convey with more tangible morphological features.

We will begin with a review of some basic terminology and concepts used in systematics.
A major school of thought regarding phylogenetic analysis is Cladistics. The word clade means branch, and thus the goal of cladistics is to determine the evolutionary branching patterns for groups of organisms. A cladistic approach to phylogenetic reconstruction is based entirely on homologous characters; characters believed to be analogous are never considered as part of the analysis. Furthermore, cladistic methods are designed to arrange organisms based on the principle of shared derived characters.

Derived characters are those that represent a change or departure from that of the ancestral character or character state, the character or character state typically found in the ancestral taxon. Derived characters, therefore, are typically considered to be advanced with respect to the primitive condition or state found in the ancestor. The primitive condition is determined by comparison with an outgroup, a taxon somewhat related to the group under study, but not as closely related to them as they all are to each other. Shared derived characters then are derived characters that are shared among two or more descendent taxa from a common ancestor.

Again, the concept of common ancestor is central to the cladistic approach because common ancestors will show homology with their descendent taxa. Cladistic analysis typically requires software to conduct the numerical computations. In any case the output is a cladogram, a branching phylogenetic tree where each branch point, or node, represents the common ancestor to the taxa represented by the two branches leading away from that node. Each descendent taxon can then be the ancestor to another pair of descendent taxa, and so on until all of the branches end at unbranched tips.

An important outcome of cladistic analysis is that only monophyletic taxa are produced, i.e., groups consist of a single ancestor and all of its descendent species. This is in contrast to paraphyletic groups (not all of the descendent species are included in a taxon) and polyphyletic groups (taxa are derived from two different lineages that do not share a recent common ancestor). Polyphyletic groupings result if a systematist groups two species that have analogous traits, i.e., traits that arose due to convergent evolution. Convergent evolution occurs when two unrelated taxa evolve similar traits because they are subject to the same selection pressures; the adaptations therefore arise independently, and do not represent true homologies.

Procedure:

You are presented with nine species of trees and must reconstruct a reasonable phylogeny for these taxa based on their morphological traits. One species is designated as the outgroup; assume that this designation is based on fossil evidence, biogeography, and morphology. You will use eight characters of the taxa to determine the best phylogeny:

Evergreenness: evergreen vs. deciduous
Leaf shape: simple vs. lobed
Leaf margins: untoothed vs. toothed
Glands on the leaf stalk (“petiolar glands”): present vs. absent
(these glands produce nectar that attracts ants, which may protect the
plant from destructive herbivores)
Fruit number per cluster: one vs. two
Fruit color: purple vs. red
Fruit texture: fuzzy vs. smooth
Leaf stalk: straight vs. curved

Build your phylogenetic tree (cladogram) by determining which character states are primitive vs. which are derived, and try to group species that have the same shared derived traits. Beware, though, that just as in real species, some species may have evolved the same traits due to convergent evolution. If you suspect that one of your characters represents an analogy, but you are not sure how to proceed, you should apply a fundamental concept in phylogenetic reconstruction, namely the principle of parsimony. The most parsimonious tree, and therefore the implied “best” tree, is the one that is shortest, that is to say, the one with the fewest number of changes in character states (and therefore, the one with the smallest number of branching points). It is important to recognize that the most parsimonious tree is not necessarily the “correct” tree in terms of faithfully representing the historical evolutionary pattern of speciation. However, the less parsimonious the tree, the lower the likelihood that it accurately depicts the real evolutionary trends of the group under investigation.

TREE SPECIES FOR PHYLOGENETIC RECONSTRUCTION

QUESTIONS:

1) For the cladogram produced in Part II, which trait(s), if any, represent analogies? How can you tell, and what evidence did you use instead to determine the best branching pattern?

2) Produce a simple matrix of taxa vs. their character states, as shown in Chapter 26 of the Campbell textbook. For each character in the matrix, use a “0” to represent ancestral character states, and a “1” to represent the derived condition. (Note: this matrix can be helpful in determining the branching patterns of your cladogram.